Starting phenix.real_space_refine on Sat Jul 4 10:07:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lx2_23564/07_2026/7lx2_23564.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lx2_23564/07_2026/7lx2_23564.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7lx2_23564/07_2026/7lx2_23564.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lx2_23564/07_2026/7lx2_23564.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lx2_23564/07_2026/7lx2_23564.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lx2_23564/07_2026/7lx2_23564.map" model { file = "/net/cci-nas-00/data/ceres_data/7lx2_23564/07_2026/7lx2_23564.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lx2_23564/07_2026/7lx2_23564.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.146 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 12645 2.51 5 N 3279 2.21 5 O 4161 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20196 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 4232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4232 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 24, 'TRANS': 509} Chain breaks: 7 Chain: "L" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 832 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "H" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1041 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "B" Number of atoms: 4232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4232 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 24, 'TRANS': 509} Chain breaks: 7 Chain: "M" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 832 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "N" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1041 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "C" Number of atoms: 4232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4232 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 24, 'TRANS': 509} Chain breaks: 7 Chain: "O" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 832 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "P" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1041 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 4.32, per 1000 atoms: 0.21 Number of scatterers: 20196 At special positions: 0 Unit cell: (152.874, 144.666, 150.822, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 111 16.00 O 4161 8.00 N 3279 7.00 C 12645 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.27 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.10 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.08 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.23 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 605 " distance=2.07 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.08 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.27 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.11 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.08 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.04 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.04 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.02 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS B 605 " distance=2.07 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.07 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.27 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.02 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.08 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.04 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS C 605 " distance=2.07 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.02 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.04 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN T 4 " - " MAN T 5 " " MAN T 5 " - " MAN T 6 " " MAN W 4 " - " MAN W 5 " " MAN h 4 " - " MAN h 5 " " MAN h 5 " - " MAN h 6 " " MAN k 4 " - " MAN k 5 " " MAN v 4 " - " MAN v 5 " " MAN v 5 " - " MAN v 6 " " MAN y 4 " - " MAN y 5 " ALPHA1-3 " BMA J 3 " - " MAN J 4 " " MAN J 4 " - " MAN J 5 " " BMA T 3 " - " MAN T 4 " " MAN T 7 " - " MAN T 8 " " BMA W 3 " - " MAN W 4 " " BMA c 3 " - " MAN c 4 " " MAN c 4 " - " MAN c 5 " " BMA h 3 " - " MAN h 4 " " MAN h 7 " - " MAN h 8 " " BMA k 3 " - " MAN k 4 " " BMA q 3 " - " MAN q 4 " " MAN q 4 " - " MAN q 5 " " BMA v 3 " - " MAN v 4 " " MAN v 7 " - " MAN v 8 " " BMA y 3 " - " MAN y 4 " ALPHA1-6 " BMA J 3 " - " MAN J 6 " " BMA T 3 " - " MAN T 7 " " MAN T 7 " - " MAN T 9 " " BMA W 3 " - " MAN W 6 " " BMA c 3 " - " MAN c 6 " " BMA h 3 " - " MAN h 7 " " MAN h 7 " - " MAN h 9 " " BMA k 3 " - " MAN k 6 " " BMA q 3 " - " MAN q 6 " " BMA v 3 " - " MAN v 7 " " MAN v 7 " - " MAN v 9 " " BMA y 3 " - " MAN y 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " NAG-ASN " NAG A 701 " - " ASN A 160 " " NAG A 702 " - " ASN A 190 " " NAG A 703 " - " ASN A 289 " " NAG A 704 " - " ASN A 339 " " NAG A 705 " - " ASN A 611 " " NAG B 701 " - " ASN B 160 " " NAG B 702 " - " ASN B 190 " " NAG B 703 " - " ASN B 289 " " NAG B 704 " - " ASN B 339 " " NAG B 705 " - " ASN B 611 " " NAG C 701 " - " ASN C 160 " " NAG C 702 " - " ASN C 190 " " NAG C 703 " - " ASN C 289 " " NAG C 704 " - " ASN C 339 " " NAG C 705 " - " ASN C 611 " " NAG D 1 " - " ASN A 88 " " NAG E 1 " - " ASN A 130 " " NAG F 1 " - " ASN A 197 " " NAG G 1 " - " ASN A 276 " " NAG I 1 " - " ASN A 301 " " NAG J 1 " - " ASN A 262 " " NAG K 1 " - " ASN A 386 " " NAG Q 1 " - " ASN A 392 " " NAG R 1 " - " ASN A 448 " " NAG S 1 " - " ASN A 295 " " NAG T 1 " - " ASN A 332 " " NAG U 1 " - " ASN A 234 " " NAG V 1 " - " ASN A 241 " " NAG W 1 " - " ASN A 138 " " NAG X 1 " - " ASN B 88 " " NAG Y 1 " - " ASN B 130 " " NAG Z 1 " - " ASN B 197 " " NAG a 1 " - " ASN B 276 " " NAG b 1 " - " ASN B 301 " " NAG c 1 " - " ASN B 262 " " NAG d 1 " - " ASN B 386 " " NAG e 1 " - " ASN B 392 " " NAG f 1 " - " ASN B 448 " " NAG g 1 " - " ASN B 295 " " NAG h 1 " - " ASN B 332 " " NAG i 1 " - " ASN B 234 " " NAG j 1 " - " ASN B 241 " " NAG k 1 " - " ASN B 138 " " NAG l 1 " - " ASN C 88 " " NAG m 1 " - " ASN C 130 " " NAG n 1 " - " ASN C 197 " " NAG o 1 " - " ASN C 276 " " NAG p 1 " - " ASN C 301 " " NAG q 1 " - " ASN C 262 " " NAG r 1 " - " ASN C 386 " " NAG s 1 " - " ASN C 392 " " NAG t 1 " - " ASN C 448 " " NAG u 1 " - " ASN C 295 " " NAG v 1 " - " ASN C 332 " " NAG w 1 " - " ASN C 234 " " NAG x 1 " - " ASN C 241 " " NAG y 1 " - " ASN C 138 " Time building additional restraints: 2.21 Conformation dependent library (CDL) restraints added in 854.4 milliseconds 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4314 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 48 sheets defined 20.5% alpha, 37.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 99 through 116 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.015A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.962A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 528 removed outlier: 4.267A pdb=" N GLY A 527 " --> pdb=" O GLY A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 542 removed outlier: 4.279A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 597 Processing helix chain 'A' and resid 618 through 625 Processing helix chain 'A' and resid 627 through 635 removed outlier: 3.654A pdb=" N LYS A 633 " --> pdb=" O MET A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 651 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 100D through 100H Processing helix chain 'B' and resid 99 through 116 Processing helix chain 'B' and resid 122 through 126 Processing helix chain 'B' and resid 335 through 348 Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 425 through 429 removed outlier: 3.957A pdb=" N GLN B 428 " --> pdb=" O ASN B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 484 removed outlier: 3.924A pdb=" N SER B 481 " --> pdb=" O ASP B 477 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.273A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 4.280A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 597 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.816A pdb=" N LYS B 633 " --> pdb=" O MET B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 651 Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 61 through 64 Processing helix chain 'N' and resid 83 through 87 Processing helix chain 'N' and resid 100D through 100H Processing helix chain 'C' and resid 99 through 117 Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.959A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.935A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 528 removed outlier: 4.283A pdb=" N GLY C 527 " --> pdb=" O GLY C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 536 through 542 removed outlier: 4.283A pdb=" N GLN C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 597 removed outlier: 3.724A pdb=" N TYR C 586 " --> pdb=" O ALA C 582 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP C 589 " --> pdb=" O ARG C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 625 Processing helix chain 'C' and resid 627 through 635 removed outlier: 3.652A pdb=" N LYS C 633 " --> pdb=" O MET C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 651 Processing helix chain 'O' and resid 79 through 83 Processing helix chain 'P' and resid 28 through 32 Processing helix chain 'P' and resid 61 through 64 Processing helix chain 'P' and resid 83 through 87 Processing helix chain 'P' and resid 100D through 100H Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.874A pdb=" N VAL A 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.053A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.760A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 132 Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.640A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.687A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.302A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.811A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.907A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 10.905A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.156A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 274 removed outlier: 11.156A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.905A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.907A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.811A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.302A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE A 359 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.602A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 8 through 13 removed outlier: 6.761A pdb=" N THR L 8 " --> pdb=" O THR L 103 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ILE L 105 " --> pdb=" O THR L 8 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL L 11 " --> pdb=" O ILE L 105 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N CYS L 88 " --> pdb=" O GLY L 99 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLY L 101 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N TYR L 86 " --> pdb=" O GLY L 101 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N TRP L 35 " --> pdb=" O ILE L 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 19 through 23 Processing sheet with id=AB4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB5, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AB6, first strand: chain 'H' and resid 58 through 59 removed outlier: 6.892A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TYR H 33 " --> pdb=" O THR H 95 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 58 through 59 removed outlier: 6.892A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TYR H 33 " --> pdb=" O THR H 95 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 494 through 499 removed outlier: 4.872A pdb=" N VAL B 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 45 through 47 removed outlier: 3.883A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL B 242 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 75 through 76 removed outlier: 3.830A pdb=" N VAL B 75 " --> pdb=" O CYS B 54 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 91 through 94 Processing sheet with id=AC3, first strand: chain 'B' and resid 130 through 132 Processing sheet with id=AC4, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AC5, first strand: chain 'B' and resid 202 through 203 removed outlier: 6.645A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 259 through 261 removed outlier: 6.709A pdb=" N LEU B 260 " --> pdb=" O THR B 450 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N GLY B 441 " --> pdb=" O ASN B 300 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ASN B 300 " --> pdb=" O GLY B 441 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLY B 451 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 10.287A pdb=" N GLU B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 11.831A pdb=" N LEU B 453 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 11.931A pdb=" N LEU B 288 " --> pdb=" O LEU B 453 " (cutoff:3.500A) removed outlier: 10.918A pdb=" N THR B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 11.173A pdb=" N VAL B 286 " --> pdb=" O THR B 455 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N GLU B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N SER B 334 " --> pdb=" O GLU B 293 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA B 329 " --> pdb=" O CYS B 418 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N PHE B 382 " --> pdb=" O LYS B 421 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 271 through 274 removed outlier: 11.173A pdb=" N VAL B 286 " --> pdb=" O THR B 455 " (cutoff:3.500A) removed outlier: 10.918A pdb=" N THR B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 11.931A pdb=" N LEU B 288 " --> pdb=" O LEU B 453 " (cutoff:3.500A) removed outlier: 11.831A pdb=" N LEU B 453 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 10.287A pdb=" N GLU B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLY B 451 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ASN B 300 " --> pdb=" O GLY B 441 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N GLY B 441 " --> pdb=" O ASN B 300 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE B 359 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 304 through 312 removed outlier: 6.582A pdb=" N GLN B 315 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 8 through 13 removed outlier: 6.730A pdb=" N THR M 8 " --> pdb=" O THR M 103 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ILE M 105 " --> pdb=" O THR M 8 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL M 11 " --> pdb=" O ILE M 105 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N GLU M 100 " --> pdb=" O CYS M 88 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N CYS M 88 " --> pdb=" O GLU M 100 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N TRP M 35 " --> pdb=" O ILE M 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 19 through 23 Processing sheet with id=AD2, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AD3, first strand: chain 'N' and resid 11 through 12 Processing sheet with id=AD4, first strand: chain 'N' and resid 58 through 59 removed outlier: 6.919A pdb=" N TRP N 36 " --> pdb=" O ILE N 48 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N TYR N 50 " --> pdb=" O TRP N 34 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP N 34 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR N 33 " --> pdb=" O THR N 95 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 58 through 59 removed outlier: 6.919A pdb=" N TRP N 36 " --> pdb=" O ILE N 48 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N TYR N 50 " --> pdb=" O TRP N 34 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP N 34 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR N 33 " --> pdb=" O THR N 95 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 494 through 499 removed outlier: 4.870A pdb=" N VAL C 36 " --> pdb=" O THR C 606 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.859A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 75 through 76 removed outlier: 3.774A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AE1, first strand: chain 'C' and resid 130 through 132 Processing sheet with id=AE2, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AE3, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.648A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.706A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.291A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.825A pdb=" N LEU C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 11.920A pdb=" N LEU C 288 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 10.908A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.171A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N GLU C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N SER C 334 " --> pdb=" O GLU C 293 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 271 through 274 removed outlier: 11.171A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.908A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.920A pdb=" N LEU C 288 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 11.825A pdb=" N LEU C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.291A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE C 359 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.611A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'O' and resid 8 through 13 removed outlier: 6.740A pdb=" N THR O 8 " --> pdb=" O THR O 103 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ILE O 105 " --> pdb=" O THR O 8 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL O 11 " --> pdb=" O ILE O 105 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TRP O 35 " --> pdb=" O ILE O 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 19 through 23 Processing sheet with id=AE9, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AF1, first strand: chain 'P' and resid 11 through 12 Processing sheet with id=AF2, first strand: chain 'P' and resid 58 through 59 removed outlier: 6.891A pdb=" N TRP P 36 " --> pdb=" O ILE P 48 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR P 50 " --> pdb=" O TRP P 34 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP P 34 " --> pdb=" O TYR P 50 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR P 33 " --> pdb=" O THR P 95 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'P' and resid 58 through 59 removed outlier: 6.891A pdb=" N TRP P 36 " --> pdb=" O ILE P 48 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR P 50 " --> pdb=" O TRP P 34 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP P 34 " --> pdb=" O TYR P 50 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR P 33 " --> pdb=" O THR P 95 " (cutoff:3.500A) 767 hydrogen bonds defined for protein. 1941 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.84 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.34: 6252 1.34 - 1.50: 7021 1.50 - 1.65: 7193 1.65 - 1.81: 128 1.81 - 1.96: 13 Bond restraints: 20607 Sorted by residual: bond pdb=" CB CYS A 247 " pdb=" SG CYS A 247 " ideal model delta sigma weight residual 1.808 1.582 0.226 3.30e-02 9.18e+02 4.71e+01 bond pdb=" NE1 TRP B 427 " pdb=" CE2 TRP B 427 " ideal model delta sigma weight residual 1.370 1.307 0.063 1.10e-02 8.26e+03 3.31e+01 bond pdb=" NE1 TRP A 427 " pdb=" CE2 TRP A 427 " ideal model delta sigma weight residual 1.370 1.307 0.063 1.10e-02 8.26e+03 3.24e+01 bond pdb=" CB CYS M 88 " pdb=" SG CYS M 88 " ideal model delta sigma weight residual 1.808 1.621 0.187 3.30e-02 9.18e+02 3.20e+01 bond pdb=" NE1 TRP C 427 " pdb=" CE2 TRP C 427 " ideal model delta sigma weight residual 1.370 1.308 0.062 1.10e-02 8.26e+03 3.14e+01 ... (remaining 20602 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 24100 2.44 - 4.87: 3472 4.87 - 7.31: 398 7.31 - 9.74: 34 9.74 - 12.18: 7 Bond angle restraints: 28011 Sorted by residual: angle pdb=" C ILE M 58 " pdb=" N PRO M 59 " pdb=" CA PRO M 59 " ideal model delta sigma weight residual 119.78 127.50 -7.72 1.03e+00 9.43e-01 5.62e+01 angle pdb=" C ARG C 298 " pdb=" N PRO C 299 " pdb=" CA PRO C 299 " ideal model delta sigma weight residual 119.87 127.65 -7.78 1.04e+00 9.25e-01 5.60e+01 angle pdb=" C ALA A 219 " pdb=" N PRO A 220 " pdb=" CA PRO A 220 " ideal model delta sigma weight residual 120.52 127.93 -7.41 9.90e-01 1.02e+00 5.59e+01 angle pdb=" C ALA B 219 " pdb=" N PRO B 220 " pdb=" CA PRO B 220 " ideal model delta sigma weight residual 120.31 127.63 -7.32 9.80e-01 1.04e+00 5.58e+01 angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.87 127.58 -7.71 1.04e+00 9.25e-01 5.50e+01 ... (remaining 28006 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.03: 10735 16.03 - 32.06: 338 32.06 - 48.09: 75 48.09 - 64.12: 50 64.12 - 80.14: 16 Dihedral angle restraints: 11214 sinusoidal: 4530 harmonic: 6684 Sorted by residual: dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 74 " pdb=" CB CYS A 74 " ideal model delta sinusoidal sigma weight residual 93.00 24.08 68.92 1 1.00e+01 1.00e-02 6.15e+01 dihedral pdb=" CB CYS B 54 " pdb=" SG CYS B 54 " pdb=" SG CYS B 74 " pdb=" CB CYS B 74 " ideal model delta sinusoidal sigma weight residual 93.00 24.58 68.42 1 1.00e+01 1.00e-02 6.07e+01 dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual 93.00 25.20 67.80 1 1.00e+01 1.00e-02 5.97e+01 ... (remaining 11211 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 2608 0.115 - 0.231: 868 0.231 - 0.346: 95 0.346 - 0.462: 7 0.462 - 0.577: 1 Chirality restraints: 3579 Sorted by residual: chirality pdb=" C1 BMA T 3 " pdb=" O4 NAG T 2 " pdb=" C2 BMA T 3 " pdb=" O5 BMA T 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.17e+01 chirality pdb=" C1 BMA h 3 " pdb=" O4 NAG h 2 " pdb=" C2 BMA h 3 " pdb=" O5 BMA h 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.12e+01 chirality pdb=" C1 BMA v 3 " pdb=" O4 NAG v 2 " pdb=" C2 BMA v 3 " pdb=" O5 BMA v 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.10e+01 ... (remaining 3576 not shown) Planarity restraints: 3393 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 190 " 0.112 2.00e-02 2.50e+03 1.15e-01 1.64e+02 pdb=" CG ASN C 190 " -0.049 2.00e-02 2.50e+03 pdb=" OD1 ASN C 190 " -0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN C 190 " -0.178 2.00e-02 2.50e+03 pdb=" C1 NAG C 702 " 0.137 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 190 " 0.112 2.00e-02 2.50e+03 1.15e-01 1.64e+02 pdb=" CG ASN A 190 " -0.049 2.00e-02 2.50e+03 pdb=" OD1 ASN A 190 " -0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN A 190 " -0.178 2.00e-02 2.50e+03 pdb=" C1 NAG A 702 " 0.137 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 190 " -0.109 2.00e-02 2.50e+03 1.12e-01 1.57e+02 pdb=" CG ASN B 190 " 0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN B 190 " 0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN B 190 " 0.174 2.00e-02 2.50e+03 pdb=" C1 NAG B 702 " -0.134 2.00e-02 2.50e+03 ... (remaining 3390 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3444 2.75 - 3.29: 17515 3.29 - 3.82: 32894 3.82 - 4.36: 39748 4.36 - 4.90: 65714 Nonbonded interactions: 159315 Sorted by model distance: nonbonded pdb=" OG1 THR B 37 " pdb=" OG1 THR B 499 " model vdw 2.211 3.040 nonbonded pdb=" OG1 THR C 37 " pdb=" OG1 THR C 499 " model vdw 2.212 3.040 nonbonded pdb=" OG1 THR A 37 " pdb=" OG1 THR A 499 " model vdw 2.212 3.040 nonbonded pdb=" O4 MAN T 5 " pdb=" O6 MAN T 5 " model vdw 2.260 3.040 nonbonded pdb=" O4 NAG b 2 " pdb=" O6 NAG b 2 " model vdw 2.267 3.040 ... (remaining 159310 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'i' selection = chain 'j' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'w' selection = chain 'x' } ncs_group { reference = chain 'H' selection = chain 'N' selection = chain 'P' } ncs_group { reference = chain 'J' selection = chain 'W' selection = chain 'c' selection = chain 'k' selection = chain 'q' selection = chain 'y' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'T' selection = chain 'h' selection = chain 'v' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 19.120 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.240 20790 Z= 1.115 Angle : 1.754 12.178 28521 Z= 1.094 Chirality : 0.104 0.577 3579 Planarity : 0.009 0.047 3336 Dihedral : 9.691 80.145 6783 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.15 % Allowed : 0.73 % Favored : 99.12 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.17), residues: 2262 helix: -1.22 (0.24), residues: 393 sheet: 1.00 (0.18), residues: 675 loop : 0.99 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 66 TYR 0.053 0.007 TYR H 100O PHE 0.043 0.007 PHE B 353 TRP 0.044 0.009 TRP A 96 HIS 0.007 0.002 HIS H 52 Details of bonding type rmsd/Z covalent geometry : bond 0.02062 / 1.07 (20607) covalent geometry : angle 1.71874 / 1.09 (28011) SS BOND : bond 0.07876 / 5.40 ( 39) SS BOND : angle 3.96237 / 2.58 ( 78) hydrogen bonds : bond 0.15876 / 10.38 ( 707) hydrogen bonds : angle 7.67387 / 5.50 ( 1941) link_ALPHA1-2 : bond 0.06013 / 3.11 ( 9) link_ALPHA1-2 : angle 2.83075 / 1.82 ( 27) link_ALPHA1-3 : bond 0.05997 / 3.49 ( 15) link_ALPHA1-3 : angle 2.75687 / 1.73 ( 45) link_ALPHA1-6 : bond 0.05672 / 3.24 ( 12) link_ALPHA1-6 : angle 3.14139 / 1.99 ( 36) link_BETA1-4 : bond 0.05711 / 3.70 ( 51) link_BETA1-4 : angle 3.65963 / 2.69 ( 153) link_NAG-ASN : bond 0.07870 / 5.01 ( 57) link_NAG-ASN : angle 2.16311 / 1.47 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 409 time to evaluate : 0.712 Fit side-chains revert: symmetry clash REVERT: A 68 VAL cc_start: 0.9181 (p) cc_final: 0.8954 (p) REVERT: B 173 TYR cc_start: 0.8034 (m-80) cc_final: 0.7809 (m-80) REVERT: N 100 LYS cc_start: 0.8460 (mttt) cc_final: 0.8218 (mmtt) outliers start: 3 outliers final: 3 residues processed: 412 average time/residue: 0.1493 time to fit residues: 91.7304 Evaluate side-chains 197 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 194 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain C residue 138 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 105 HIS A 229 ASN L 52 ASN B 105 HIS B 625 ASN M 52 ASN C 105 HIS C 114 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.148956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.106896 restraints weight = 26982.854| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 3.20 r_work: 0.3238 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 20790 Z= 0.210 Angle : 0.756 10.922 28521 Z= 0.375 Chirality : 0.049 0.329 3579 Planarity : 0.004 0.028 3336 Dihedral : 4.910 22.538 2484 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.06 % Favored : 98.81 % Rotamer: Outliers : 1.75 % Allowed : 5.60 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.17), residues: 2262 helix: 0.25 (0.26), residues: 384 sheet: 0.70 (0.18), residues: 687 loop : 0.50 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 273 TYR 0.016 0.002 TYR C 318 PHE 0.016 0.003 PHE A 383 TRP 0.018 0.002 TRP A 479 HIS 0.006 0.001 HIS P 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.21 (20607) covalent geometry : angle 0.70958 / 0.37 (28011) SS BOND : bond 0.00398 / 0.28 ( 39) SS BOND : angle 1.80819 / 1.16 ( 78) hydrogen bonds : bond 0.05123 / 3.37 ( 707) hydrogen bonds : angle 5.99404 / 4.30 ( 1941) link_ALPHA1-2 : bond 0.00634 / 0.30 ( 9) link_ALPHA1-2 : angle 1.64578 / 0.90 ( 27) link_ALPHA1-3 : bond 0.00808 / 0.48 ( 15) link_ALPHA1-3 : angle 1.47935 / 0.85 ( 45) link_ALPHA1-6 : bond 0.00685 / 0.41 ( 12) link_ALPHA1-6 : angle 1.41102 / 0.84 ( 36) link_BETA1-4 : bond 0.00701 / 0.44 ( 51) link_BETA1-4 : angle 2.49428 / 1.81 ( 153) link_NAG-ASN : bond 0.00320 / 0.21 ( 57) link_NAG-ASN : angle 2.11329 / 1.52 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 240 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.8072 (tpp) cc_final: 0.7779 (mmp) REVERT: A 648 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7480 (mp0) REVERT: B 173 TYR cc_start: 0.8403 (m-80) cc_final: 0.8162 (m-80) REVERT: B 246 GLN cc_start: 0.8489 (mt0) cc_final: 0.8018 (tp40) REVERT: B 296 CYS cc_start: 0.7436 (m) cc_final: 0.7210 (m) REVERT: N 99 ARG cc_start: 0.7903 (ttp-110) cc_final: 0.7701 (ttm110) REVERT: N 100 LYS cc_start: 0.8493 (mttt) cc_final: 0.8027 (mmtt) REVERT: N 100 MET cc_start: 0.8383 (mpp) cc_final: 0.7483 (mpp) REVERT: C 246 GLN cc_start: 0.8512 (mt0) cc_final: 0.8009 (tp-100) REVERT: P 100 LYS cc_start: 0.8487 (mttp) cc_final: 0.8245 (mmtm) outliers start: 36 outliers final: 14 residues processed: 271 average time/residue: 0.1341 time to fit residues: 55.8710 Evaluate side-chains 196 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 182 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 109 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 211 optimal weight: 8.9990 chunk 54 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 167 optimal weight: 0.9980 chunk 206 optimal weight: 10.0000 chunk 128 optimal weight: 0.8980 chunk 118 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 ASN L 52 ASN N 3 HIS C 94 ASN C 362 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.143488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.101671 restraints weight = 26510.672| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 3.41 r_work: 0.3102 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20790 Z= 0.148 Angle : 0.625 8.740 28521 Z= 0.309 Chirality : 0.045 0.214 3579 Planarity : 0.003 0.037 3336 Dihedral : 4.597 26.610 2478 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.34 % Allowed : 7.41 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.17), residues: 2262 helix: 0.82 (0.27), residues: 384 sheet: 0.62 (0.19), residues: 669 loop : 0.21 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 30 TYR 0.011 0.001 TYR L 86 PHE 0.014 0.002 PHE B 53 TRP 0.015 0.001 TRP C 479 HIS 0.008 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (20607) covalent geometry : angle 0.58942 / 0.30 (28011) SS BOND : bond 0.00373 / 0.23 ( 39) SS BOND : angle 1.75122 / 1.04 ( 78) hydrogen bonds : bond 0.03883 / 2.54 ( 707) hydrogen bonds : angle 5.45511 / 3.92 ( 1941) link_ALPHA1-2 : bond 0.00622 / 0.29 ( 9) link_ALPHA1-2 : angle 1.52043 / 0.88 ( 27) link_ALPHA1-3 : bond 0.00665 / 0.39 ( 15) link_ALPHA1-3 : angle 1.48100 / 0.89 ( 45) link_ALPHA1-6 : bond 0.00602 / 0.36 ( 12) link_ALPHA1-6 : angle 1.36670 / 0.82 ( 36) link_BETA1-4 : bond 0.00648 / 0.41 ( 51) link_BETA1-4 : angle 1.95668 / 1.42 ( 153) link_NAG-ASN : bond 0.00210 / 0.14 ( 57) link_NAG-ASN : angle 1.45267 / 0.99 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 192 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.7759 (tpp) cc_final: 0.6876 (mmm) REVERT: H 28 LEU cc_start: 0.7710 (mt) cc_final: 0.7379 (tp) REVERT: H 100 LYS cc_start: 0.8250 (mttm) cc_final: 0.8029 (mmtt) REVERT: B 173 TYR cc_start: 0.8451 (m-80) cc_final: 0.8190 (m-80) REVERT: B 246 GLN cc_start: 0.8457 (mt0) cc_final: 0.7866 (tp-100) REVERT: B 620 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.8135 (t0) REVERT: N 100 LYS cc_start: 0.8332 (mttt) cc_final: 0.7790 (mmmt) REVERT: N 100 MET cc_start: 0.8152 (mpp) cc_final: 0.7272 (mpp) REVERT: C 95 MET cc_start: 0.9070 (ptm) cc_final: 0.8813 (ptm) REVERT: C 246 GLN cc_start: 0.8582 (mt0) cc_final: 0.8038 (tp-100) REVERT: C 475 MET cc_start: 0.7918 (mmt) cc_final: 0.7627 (mmt) REVERT: C 581 LEU cc_start: 0.8456 (mt) cc_final: 0.8121 (mt) REVERT: P 100 LYS cc_start: 0.8211 (mttp) cc_final: 0.7929 (mmtm) outliers start: 48 outliers final: 22 residues processed: 225 average time/residue: 0.1483 time to fit residues: 51.8998 Evaluate side-chains 192 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 620 ASP Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain N residue 41 LEU Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 109 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 153 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 220 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 223 optimal weight: 30.0000 chunk 182 optimal weight: 6.9990 chunk 204 optimal weight: 0.6980 chunk 208 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 200 optimal weight: 9.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 GLN L 52 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.139852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.100751 restraints weight = 26372.392| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 3.44 r_work: 0.3092 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20790 Z= 0.158 Angle : 0.608 8.031 28521 Z= 0.296 Chirality : 0.045 0.185 3579 Planarity : 0.004 0.037 3336 Dihedral : 4.485 25.691 2478 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.85 % Allowed : 8.28 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.17), residues: 2262 helix: 0.98 (0.28), residues: 384 sheet: 0.38 (0.18), residues: 699 loop : 0.08 (0.17), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 31 TYR 0.012 0.001 TYR N 100O PHE 0.013 0.002 PHE B 53 TRP 0.012 0.001 TRP C 479 HIS 0.009 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (20607) covalent geometry : angle 0.57156 / 0.29 (28011) SS BOND : bond 0.00427 / 0.24 ( 39) SS BOND : angle 1.69229 / 1.03 ( 78) hydrogen bonds : bond 0.03645 / 2.38 ( 707) hydrogen bonds : angle 5.24062 / 3.76 ( 1941) link_ALPHA1-2 : bond 0.00553 / 0.26 ( 9) link_ALPHA1-2 : angle 1.56382 / 0.90 ( 27) link_ALPHA1-3 : bond 0.00571 / 0.34 ( 15) link_ALPHA1-3 : angle 1.52373 / 0.91 ( 45) link_ALPHA1-6 : bond 0.00490 / 0.29 ( 12) link_ALPHA1-6 : angle 1.38322 / 0.82 ( 36) link_BETA1-4 : bond 0.00601 / 0.38 ( 51) link_BETA1-4 : angle 1.91790 / 1.40 ( 153) link_NAG-ASN : bond 0.00222 / 0.15 ( 57) link_NAG-ASN : angle 1.44261 / 0.99 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 180 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.7562 (tpp) cc_final: 0.6592 (mmm) REVERT: A 620 ASP cc_start: 0.8359 (t0) cc_final: 0.7726 (t0) REVERT: H 28 LEU cc_start: 0.7460 (mt) cc_final: 0.7191 (tp) REVERT: H 99 ARG cc_start: 0.8058 (ttm110) cc_final: 0.7777 (ttm110) REVERT: B 173 TYR cc_start: 0.8471 (m-80) cc_final: 0.8239 (m-80) REVERT: B 246 GLN cc_start: 0.8418 (mt0) cc_final: 0.7763 (tp-100) REVERT: N 99 ARG cc_start: 0.8243 (ttp-110) cc_final: 0.7524 (ttm110) REVERT: N 100 LYS cc_start: 0.8204 (mttt) cc_final: 0.7591 (mmmt) REVERT: C 246 GLN cc_start: 0.8443 (mt0) cc_final: 0.7716 (tp-100) REVERT: C 475 MET cc_start: 0.7630 (mmt) cc_final: 0.7290 (mmt) REVERT: C 581 LEU cc_start: 0.8318 (mt) cc_final: 0.7995 (mt) REVERT: P 100 LYS cc_start: 0.8040 (mttp) cc_final: 0.7601 (mmtt) outliers start: 38 outliers final: 25 residues processed: 211 average time/residue: 0.1496 time to fit residues: 48.4676 Evaluate side-chains 195 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain N residue 41 LEU Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 109 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 136 optimal weight: 10.0000 chunk 217 optimal weight: 20.0000 chunk 130 optimal weight: 9.9990 chunk 19 optimal weight: 0.6980 chunk 131 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 141 optimal weight: 20.0000 chunk 32 optimal weight: 0.9990 chunk 173 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.147163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.105300 restraints weight = 27138.787| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 3.19 r_work: 0.3218 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20790 Z= 0.153 Angle : 0.594 7.828 28521 Z= 0.289 Chirality : 0.044 0.179 3579 Planarity : 0.003 0.038 3336 Dihedral : 4.406 24.680 2478 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.10 % Allowed : 8.04 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.17), residues: 2262 helix: 1.07 (0.28), residues: 384 sheet: 0.38 (0.18), residues: 699 loop : 0.01 (0.17), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 500 TYR 0.011 0.001 TYR H 100O PHE 0.014 0.002 PHE B 53 TRP 0.010 0.001 TRP C 112 HIS 0.009 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.15 (20607) covalent geometry : angle 0.55598 / 0.28 (28011) SS BOND : bond 0.00404 / 0.24 ( 39) SS BOND : angle 1.97395 / 1.12 ( 78) hydrogen bonds : bond 0.03480 / 2.28 ( 707) hydrogen bonds : angle 5.14673 / 3.68 ( 1941) link_ALPHA1-2 : bond 0.00569 / 0.27 ( 9) link_ALPHA1-2 : angle 1.55345 / 0.90 ( 27) link_ALPHA1-3 : bond 0.00555 / 0.33 ( 15) link_ALPHA1-3 : angle 1.55339 / 0.93 ( 45) link_ALPHA1-6 : bond 0.00470 / 0.28 ( 12) link_ALPHA1-6 : angle 1.38842 / 0.82 ( 36) link_BETA1-4 : bond 0.00598 / 0.37 ( 51) link_BETA1-4 : angle 1.87081 / 1.36 ( 153) link_NAG-ASN : bond 0.00203 / 0.13 ( 57) link_NAG-ASN : angle 1.39059 / 0.95 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 173 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.7856 (tpp) cc_final: 0.7409 (mmp) REVERT: A 620 ASP cc_start: 0.8380 (t0) cc_final: 0.7827 (t0) REVERT: H 28 LEU cc_start: 0.7661 (mt) cc_final: 0.7381 (tp) REVERT: H 99 ARG cc_start: 0.8084 (ttm110) cc_final: 0.7836 (ttm110) REVERT: B 173 TYR cc_start: 0.8476 (m-80) cc_final: 0.8262 (m-80) REVERT: B 246 GLN cc_start: 0.8591 (mt0) cc_final: 0.8038 (tp-100) REVERT: N 100 LYS cc_start: 0.8511 (mttt) cc_final: 0.7953 (mmmt) REVERT: C 246 GLN cc_start: 0.8674 (mt0) cc_final: 0.8146 (tp-100) REVERT: C 475 MET cc_start: 0.7877 (mmt) cc_final: 0.7583 (mmt) REVERT: C 581 LEU cc_start: 0.8647 (mt) cc_final: 0.8331 (mt) REVERT: P 100 LYS cc_start: 0.8496 (mttp) cc_final: 0.8062 (mmtt) outliers start: 43 outliers final: 31 residues processed: 206 average time/residue: 0.1431 time to fit residues: 46.1139 Evaluate side-chains 202 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 171 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain N residue 92 CYS Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 648 GLU Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 109 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 12 optimal weight: 0.9990 chunk 99 optimal weight: 7.9990 chunk 177 optimal weight: 6.9990 chunk 217 optimal weight: 20.0000 chunk 156 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 163 optimal weight: 0.0010 chunk 199 optimal weight: 4.9990 chunk 204 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 overall best weight: 1.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.148628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.106991 restraints weight = 26930.328| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 3.17 r_work: 0.3185 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20790 Z= 0.115 Angle : 0.557 7.579 28521 Z= 0.271 Chirality : 0.043 0.167 3579 Planarity : 0.003 0.034 3336 Dihedral : 4.243 25.180 2478 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.80 % Allowed : 8.58 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.17), residues: 2262 helix: 1.32 (0.28), residues: 384 sheet: 0.45 (0.18), residues: 723 loop : 0.04 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 95 TYR 0.011 0.001 TYR H 33 PHE 0.012 0.001 PHE B 53 TRP 0.011 0.001 TRP H 34 HIS 0.009 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.11 (20607) covalent geometry : angle 0.52234 / 0.26 (28011) SS BOND : bond 0.00372 / 0.23 ( 39) SS BOND : angle 1.64400 / 0.96 ( 78) hydrogen bonds : bond 0.03110 / 2.04 ( 707) hydrogen bonds : angle 4.95226 / 3.53 ( 1941) link_ALPHA1-2 : bond 0.00616 / 0.29 ( 9) link_ALPHA1-2 : angle 1.51194 / 0.88 ( 27) link_ALPHA1-3 : bond 0.00570 / 0.34 ( 15) link_ALPHA1-3 : angle 1.52991 / 0.92 ( 45) link_ALPHA1-6 : bond 0.00499 / 0.30 ( 12) link_ALPHA1-6 : angle 1.37835 / 0.82 ( 36) link_BETA1-4 : bond 0.00607 / 0.38 ( 51) link_BETA1-4 : angle 1.78252 / 1.30 ( 153) link_NAG-ASN : bond 0.00166 / 0.11 ( 57) link_NAG-ASN : angle 1.25210 / 0.85 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 171 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.7794 (tpp) cc_final: 0.7191 (mmt) REVERT: A 620 ASP cc_start: 0.8419 (t0) cc_final: 0.7812 (t0) REVERT: H 28 LEU cc_start: 0.7585 (mt) cc_final: 0.7338 (tp) REVERT: H 99 ARG cc_start: 0.8101 (ttm110) cc_final: 0.7857 (ttm110) REVERT: B 51 THR cc_start: 0.9345 (m) cc_final: 0.9140 (p) REVERT: B 173 TYR cc_start: 0.8517 (m-80) cc_final: 0.8306 (m-80) REVERT: B 246 GLN cc_start: 0.8550 (mt0) cc_final: 0.8029 (tp-100) REVERT: N 99 ARG cc_start: 0.8241 (ttp-110) cc_final: 0.7807 (ttp80) REVERT: N 100 LYS cc_start: 0.8488 (mttt) cc_final: 0.7915 (mmmt) REVERT: C 109 ILE cc_start: 0.8270 (mm) cc_final: 0.7852 (mt) REVERT: C 246 GLN cc_start: 0.8663 (mt0) cc_final: 0.8139 (tp-100) REVERT: C 475 MET cc_start: 0.7767 (mmt) cc_final: 0.7448 (mmt) REVERT: C 581 LEU cc_start: 0.8565 (mt) cc_final: 0.8270 (mt) REVERT: P 100 LYS cc_start: 0.8479 (mttp) cc_final: 0.8032 (mmtt) outliers start: 37 outliers final: 28 residues processed: 200 average time/residue: 0.1432 time to fit residues: 44.4790 Evaluate side-chains 192 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 164 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 648 GLU Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 109 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 76 optimal weight: 6.9990 chunk 131 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 chunk 180 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 213 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 chunk 204 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.147532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.105784 restraints weight = 27225.309| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 3.19 r_work: 0.3223 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20790 Z= 0.134 Angle : 0.565 7.257 28521 Z= 0.274 Chirality : 0.043 0.172 3579 Planarity : 0.003 0.037 3336 Dihedral : 4.203 24.720 2478 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.05 % Allowed : 8.72 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.17), residues: 2262 helix: 1.41 (0.28), residues: 384 sheet: 0.47 (0.18), residues: 720 loop : -0.01 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 95 TYR 0.011 0.001 TYR N 33 PHE 0.013 0.002 PHE N 100K TRP 0.009 0.001 TRP B 479 HIS 0.009 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.13 (20607) covalent geometry : angle 0.52996 / 0.27 (28011) SS BOND : bond 0.00355 / 0.22 ( 39) SS BOND : angle 1.62306 / 0.97 ( 78) hydrogen bonds : bond 0.03206 / 2.10 ( 707) hydrogen bonds : angle 4.94170 / 3.53 ( 1941) link_ALPHA1-2 : bond 0.00556 / 0.26 ( 9) link_ALPHA1-2 : angle 1.51945 / 0.88 ( 27) link_ALPHA1-3 : bond 0.00513 / 0.30 ( 15) link_ALPHA1-3 : angle 1.56532 / 0.94 ( 45) link_ALPHA1-6 : bond 0.00449 / 0.27 ( 12) link_ALPHA1-6 : angle 1.40270 / 0.83 ( 36) link_BETA1-4 : bond 0.00578 / 0.36 ( 51) link_BETA1-4 : angle 1.79982 / 1.31 ( 153) link_NAG-ASN : bond 0.00189 / 0.12 ( 57) link_NAG-ASN : angle 1.30500 / 0.89 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 169 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.7809 (tpp) cc_final: 0.7242 (mmt) REVERT: A 620 ASP cc_start: 0.8365 (t0) cc_final: 0.7744 (t0) REVERT: H 99 ARG cc_start: 0.8140 (ttm110) cc_final: 0.7897 (ttm110) REVERT: B 46 LYS cc_start: 0.8433 (ptmm) cc_final: 0.8061 (pttp) REVERT: B 173 TYR cc_start: 0.8490 (m-80) cc_final: 0.8281 (m-80) REVERT: B 246 GLN cc_start: 0.8585 (mt0) cc_final: 0.8119 (tp-100) REVERT: N 99 ARG cc_start: 0.8248 (ttp-110) cc_final: 0.7837 (ttp80) REVERT: N 100 LYS cc_start: 0.8520 (mttt) cc_final: 0.7936 (mmtt) REVERT: C 246 GLN cc_start: 0.8616 (mt0) cc_final: 0.8062 (tp-100) REVERT: C 475 MET cc_start: 0.7812 (mmt) cc_final: 0.7474 (mmt) REVERT: C 581 LEU cc_start: 0.8645 (mt) cc_final: 0.8348 (mt) REVERT: O 31 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.7811 (mtp180) REVERT: P 100 LYS cc_start: 0.8489 (mttp) cc_final: 0.8163 (mmtt) outliers start: 42 outliers final: 33 residues processed: 201 average time/residue: 0.1562 time to fit residues: 47.6609 Evaluate side-chains 197 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 163 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain N residue 92 CYS Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 648 GLU Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 109 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 110 optimal weight: 0.6980 chunk 68 optimal weight: 10.0000 chunk 217 optimal weight: 20.0000 chunk 197 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 193 optimal weight: 0.5980 chunk 181 optimal weight: 4.9990 chunk 158 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.147099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.105329 restraints weight = 27130.866| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 3.18 r_work: 0.3211 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20790 Z= 0.145 Angle : 0.567 7.268 28521 Z= 0.275 Chirality : 0.044 0.163 3579 Planarity : 0.003 0.037 3336 Dihedral : 4.213 24.543 2478 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.90 % Allowed : 9.11 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.17), residues: 2262 helix: 1.38 (0.28), residues: 387 sheet: 0.46 (0.19), residues: 726 loop : -0.02 (0.18), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 500 TYR 0.011 0.001 TYR P 100M PHE 0.012 0.002 PHE N 100K TRP 0.009 0.001 TRP H 34 HIS 0.009 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.14 (20607) covalent geometry : angle 0.53286 / 0.27 (28011) SS BOND : bond 0.00376 / 0.24 ( 39) SS BOND : angle 1.53432 / 0.91 ( 78) hydrogen bonds : bond 0.03224 / 2.11 ( 707) hydrogen bonds : angle 4.95489 / 3.54 ( 1941) link_ALPHA1-2 : bond 0.00563 / 0.27 ( 9) link_ALPHA1-2 : angle 1.52181 / 0.88 ( 27) link_ALPHA1-3 : bond 0.00506 / 0.30 ( 15) link_ALPHA1-3 : angle 1.56880 / 0.94 ( 45) link_ALPHA1-6 : bond 0.00419 / 0.25 ( 12) link_ALPHA1-6 : angle 1.41460 / 0.83 ( 36) link_BETA1-4 : bond 0.00594 / 0.37 ( 51) link_BETA1-4 : angle 1.80350 / 1.32 ( 153) link_NAG-ASN : bond 0.00186 / 0.12 ( 57) link_NAG-ASN : angle 1.30835 / 0.89 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 169 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.7833 (tpp) cc_final: 0.7214 (mmt) REVERT: A 620 ASP cc_start: 0.8379 (t0) cc_final: 0.7762 (t0) REVERT: L 95 ASN cc_start: 0.7719 (m-40) cc_final: 0.7211 (t0) REVERT: H 99 ARG cc_start: 0.8113 (ttm110) cc_final: 0.7884 (ttm110) REVERT: B 46 LYS cc_start: 0.8436 (ptmm) cc_final: 0.8050 (pttp) REVERT: B 95 MET cc_start: 0.9051 (ptm) cc_final: 0.8697 (ptm) REVERT: B 173 TYR cc_start: 0.8501 (m-80) cc_final: 0.8291 (m-80) REVERT: B 246 GLN cc_start: 0.8572 (mt0) cc_final: 0.8081 (tp-100) REVERT: B 475 MET cc_start: 0.7701 (mmt) cc_final: 0.7392 (mmt) REVERT: N 99 ARG cc_start: 0.8258 (ttp-110) cc_final: 0.7855 (ttp80) REVERT: N 100 LYS cc_start: 0.8511 (mttt) cc_final: 0.7916 (mmtt) REVERT: C 246 GLN cc_start: 0.8599 (mt0) cc_final: 0.8064 (tp-100) REVERT: C 475 MET cc_start: 0.7774 (mmt) cc_final: 0.7423 (mmt) REVERT: C 581 LEU cc_start: 0.8642 (mt) cc_final: 0.8330 (mt) REVERT: O 31 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.7908 (mtp180) REVERT: O 36 TYR cc_start: 0.8494 (m-80) cc_final: 0.8291 (m-80) REVERT: P 100 LYS cc_start: 0.8478 (mttp) cc_final: 0.8147 (mmtt) outliers start: 39 outliers final: 33 residues processed: 201 average time/residue: 0.1389 time to fit residues: 43.2724 Evaluate side-chains 196 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 162 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain N residue 92 CYS Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 648 GLU Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 92 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 85 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 109 optimal weight: 6.9990 chunk 157 optimal weight: 0.9990 chunk 117 optimal weight: 0.5980 chunk 208 optimal weight: 20.0000 chunk 148 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 201 optimal weight: 0.9980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.147622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.105948 restraints weight = 27033.211| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 3.18 r_work: 0.3173 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20790 Z= 0.126 Angle : 0.556 7.203 28521 Z= 0.270 Chirality : 0.043 0.161 3579 Planarity : 0.003 0.035 3336 Dihedral : 4.176 23.984 2478 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.85 % Allowed : 9.21 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.17), residues: 2262 helix: 1.46 (0.28), residues: 387 sheet: 0.49 (0.19), residues: 708 loop : -0.08 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 95 TYR 0.011 0.001 TYR N 33 PHE 0.012 0.001 PHE C 53 TRP 0.010 0.001 TRP N 36 HIS 0.009 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (20607) covalent geometry : angle 0.52207 / 0.26 (28011) SS BOND : bond 0.00362 / 0.23 ( 39) SS BOND : angle 1.55566 / 0.94 ( 78) hydrogen bonds : bond 0.03100 / 2.04 ( 707) hydrogen bonds : angle 4.89831 / 3.50 ( 1941) link_ALPHA1-2 : bond 0.00592 / 0.28 ( 9) link_ALPHA1-2 : angle 1.50912 / 0.88 ( 27) link_ALPHA1-3 : bond 0.00517 / 0.30 ( 15) link_ALPHA1-3 : angle 1.56133 / 0.94 ( 45) link_ALPHA1-6 : bond 0.00432 / 0.25 ( 12) link_ALPHA1-6 : angle 1.40507 / 0.83 ( 36) link_BETA1-4 : bond 0.00595 / 0.37 ( 51) link_BETA1-4 : angle 1.77377 / 1.29 ( 153) link_NAG-ASN : bond 0.00169 / 0.11 ( 57) link_NAG-ASN : angle 1.27132 / 0.86 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 161 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.7806 (tpp) cc_final: 0.7209 (mmt) REVERT: A 620 ASP cc_start: 0.8377 (t0) cc_final: 0.7756 (t0) REVERT: L 95 ASN cc_start: 0.7664 (m-40) cc_final: 0.7143 (t0) REVERT: H 99 ARG cc_start: 0.8119 (ttm110) cc_final: 0.7891 (ttm110) REVERT: B 46 LYS cc_start: 0.8426 (ptmm) cc_final: 0.8037 (pttp) REVERT: B 173 TYR cc_start: 0.8496 (m-80) cc_final: 0.8281 (m-80) REVERT: B 246 GLN cc_start: 0.8550 (mt0) cc_final: 0.8200 (tp-100) REVERT: N 99 ARG cc_start: 0.8176 (ttp-110) cc_final: 0.7768 (ttp80) REVERT: N 100 LYS cc_start: 0.8496 (mttt) cc_final: 0.7889 (mmtt) REVERT: C 246 GLN cc_start: 0.8574 (mt0) cc_final: 0.8047 (tp-100) REVERT: C 475 MET cc_start: 0.7717 (mmt) cc_final: 0.7359 (mmt) REVERT: C 581 LEU cc_start: 0.8600 (mt) cc_final: 0.8300 (mt) REVERT: O 31 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.7919 (mtp180) REVERT: O 36 TYR cc_start: 0.8471 (m-80) cc_final: 0.8263 (m-80) REVERT: P 100 LYS cc_start: 0.8466 (mttp) cc_final: 0.8135 (mmtt) outliers start: 38 outliers final: 32 residues processed: 193 average time/residue: 0.1518 time to fit residues: 44.8136 Evaluate side-chains 193 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain N residue 92 CYS Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 648 GLU Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 92 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 16 optimal weight: 0.1980 chunk 187 optimal weight: 4.9990 chunk 139 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 171 optimal weight: 4.9990 chunk 65 optimal weight: 40.0000 chunk 70 optimal weight: 9.9990 chunk 145 optimal weight: 7.9990 chunk 191 optimal weight: 3.9990 chunk 176 optimal weight: 0.9980 chunk 168 optimal weight: 0.8980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.147263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.105550 restraints weight = 27251.310| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 3.20 r_work: 0.3167 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20790 Z= 0.135 Angle : 0.560 7.095 28521 Z= 0.272 Chirality : 0.043 0.159 3579 Planarity : 0.003 0.036 3336 Dihedral : 4.170 24.040 2478 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.75 % Allowed : 9.45 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.17), residues: 2262 helix: 1.48 (0.28), residues: 387 sheet: 0.51 (0.19), residues: 708 loop : -0.11 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 500 TYR 0.011 0.001 TYR P 100M PHE 0.012 0.002 PHE N 100K TRP 0.010 0.001 TRP N 36 HIS 0.009 0.001 HIS B 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.13 (20607) covalent geometry : angle 0.52648 / 0.26 (28011) SS BOND : bond 0.00369 / 0.23 ( 39) SS BOND : angle 1.50874 / 0.90 ( 78) hydrogen bonds : bond 0.03115 / 2.04 ( 707) hydrogen bonds : angle 4.89157 / 3.49 ( 1941) link_ALPHA1-2 : bond 0.00573 / 0.27 ( 9) link_ALPHA1-2 : angle 1.50640 / 0.88 ( 27) link_ALPHA1-3 : bond 0.00505 / 0.30 ( 15) link_ALPHA1-3 : angle 1.56135 / 0.93 ( 45) link_ALPHA1-6 : bond 0.00411 / 0.24 ( 12) link_ALPHA1-6 : angle 1.41441 / 0.83 ( 36) link_BETA1-4 : bond 0.00591 / 0.37 ( 51) link_BETA1-4 : angle 1.77693 / 1.29 ( 153) link_NAG-ASN : bond 0.00176 / 0.11 ( 57) link_NAG-ASN : angle 1.29344 / 0.87 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 170 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.7814 (tpp) cc_final: 0.7267 (mmt) REVERT: A 620 ASP cc_start: 0.8396 (t0) cc_final: 0.7781 (t0) REVERT: L 95 ASN cc_start: 0.7682 (m-40) cc_final: 0.7172 (t0) REVERT: H 99 ARG cc_start: 0.8137 (ttm110) cc_final: 0.7898 (ttm110) REVERT: B 173 TYR cc_start: 0.8503 (m-80) cc_final: 0.8289 (m-80) REVERT: B 246 GLN cc_start: 0.8571 (mt0) cc_final: 0.8198 (tp-100) REVERT: N 99 ARG cc_start: 0.8198 (ttp-110) cc_final: 0.7805 (ttp80) REVERT: N 100 LYS cc_start: 0.8499 (mttt) cc_final: 0.8001 (mmtt) REVERT: C 246 GLN cc_start: 0.8562 (mt0) cc_final: 0.8095 (tp-100) REVERT: C 475 MET cc_start: 0.7720 (mmt) cc_final: 0.7359 (mmt) REVERT: C 581 LEU cc_start: 0.8613 (mt) cc_final: 0.8308 (mt) REVERT: O 31 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.7937 (mtp180) REVERT: O 36 TYR cc_start: 0.8480 (m-80) cc_final: 0.8269 (m-80) REVERT: P 5 GLN cc_start: 0.8493 (mm-40) cc_final: 0.8048 (mm110) REVERT: P 100 LYS cc_start: 0.8448 (mttp) cc_final: 0.8116 (mmtt) outliers start: 36 outliers final: 32 residues processed: 199 average time/residue: 0.1485 time to fit residues: 45.4117 Evaluate side-chains 195 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain N residue 92 CYS Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 648 GLU Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 92 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 44 optimal weight: 6.9990 chunk 176 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 129 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 156 optimal weight: 0.1980 chunk 57 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 45 optimal weight: 0.2980 chunk 25 optimal weight: 2.9990 chunk 225 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.148081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.106550 restraints weight = 27121.369| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 3.18 r_work: 0.3182 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20790 Z= 0.118 Angle : 0.558 10.181 28521 Z= 0.272 Chirality : 0.043 0.158 3579 Planarity : 0.003 0.034 3336 Dihedral : 4.193 32.978 2478 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.61 % Allowed : 9.75 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.18), residues: 2262 helix: 1.55 (0.28), residues: 387 sheet: 0.56 (0.19), residues: 708 loop : -0.09 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 95 TYR 0.011 0.001 TYR N 33 PHE 0.013 0.001 PHE A 53 TRP 0.013 0.001 TRP P 34 HIS 0.008 0.001 HIS B 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (20607) covalent geometry : angle 0.52119 / 0.26 (28011) SS BOND : bond 0.00374 / 0.25 ( 39) SS BOND : angle 1.98462 / 1.24 ( 78) hydrogen bonds : bond 0.02999 / 1.97 ( 707) hydrogen bonds : angle 4.85150 / 3.46 ( 1941) link_ALPHA1-2 : bond 0.00606 / 0.29 ( 9) link_ALPHA1-2 : angle 1.49413 / 0.87 ( 27) link_ALPHA1-3 : bond 0.00522 / 0.31 ( 15) link_ALPHA1-3 : angle 1.55573 / 0.93 ( 45) link_ALPHA1-6 : bond 0.00430 / 0.25 ( 12) link_ALPHA1-6 : angle 1.40538 / 0.83 ( 36) link_BETA1-4 : bond 0.00595 / 0.37 ( 51) link_BETA1-4 : angle 1.74286 / 1.27 ( 153) link_NAG-ASN : bond 0.00159 / 0.10 ( 57) link_NAG-ASN : angle 1.24512 / 0.84 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4056.01 seconds wall clock time: 70 minutes 42.36 seconds (4242.36 seconds total)